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BatchJobs (version 1.8)

Batch Computing with R

Description

Provides Map, Reduce and Filter variants to generate jobs on batch computing systems like PBS/Torque, LSF, SLURM and Sun Grid Engine. Multicore and SSH systems are also supported. For further details see the project web page.

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Install

install.packages('BatchJobs')

Monthly Downloads

985

Version

1.8

License

BSD_2_clause + file LICENSE

Issues

Pull Requests

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Repository

https://github.com/tudo-r/BatchJobs

Maintainer

Bernd Bischl

Last Published

May 14th, 2019

Functions in BatchJobs (1.8)

batchExpandGrid

Map function over all combinations.

cfReadBrewTemplate

Cluster functions helper: Read in your brew template file.

callFunctionOnSSHWorkers

Call an arbitrary function on specified SSH workers.

makeClusterFunctionsSSH

Create an SSH cluster to execute jobs.

Function to get job resources in job function.

Construct a registry object.

Creates a job description.

getSSHWorkersInfo

Print and return R installation and other information for SSH workers.

Display the contents of a log file.

makeClusterFunctionsTorque

Create cluster functions for torque-based systems.

Cluster functions helper: Brew your template into a job description file.

Helper function to debug multicore mode.

Retrieve or show status information about jobs.

addRegistrySourceDirs

Add source dirs to registry.

cfHandleUnknownSubmitError

Cluster functions helper: Handle an unknown error during job submission.

Sweep obsolete files from the file system.

Find all results where a specific condition is true.

Manually query the BatchJobs database

Reduces via a binary function over a list adding jobs to a registry.

addRegistrySourceFiles

Add source files to registry.

Finds ids of jobs that match a query.

Helper function to debug SSH mode.

Cluster functions helper: Kill a batch job via OS command

Unload exported R objects.

Find jobs depending on computional state.

getErrorMessages

Get error messages of jobs.

BatchJobs configuration.

Returns a list of BatchJobs configuration settings

Syncronize staged queries into the registry.

Get the physical location of job files on the hard disk.

copyRequiredJobFiles

ONLY FOR INTERNAL USAGE.

Get ids of jobs in registry.

Retrieve Job Parameters.

Get number of jobs in registry.

Get computational information of jobs.

makeClusterFunctionsSLURM

Create cluster functions for SLURM-based systems.

makeClusterFunctionsSGE

Create cluster functions for Sun Grid Engine systems.

Reduce results from result directory.

getJobResources

Function to get the resources that were submitted for some jobs.

Remove a registry object.

Load exported R data objects.

Sanitize a path

Kill some jobs on the batch system.

Load a specific configuration file.

Get jobs from registry by id.

Get log file paths for jobs.

ONLY FOR INTERNAL USAGE.

dbCreateJobDefTable

ONLY FOR INTERNAL USAGE.

Load a previously saved registry.

removeRegistrySourceFiles

Remove source files from registry.

Loads a specific result file.

setRegistryPackages

Set packages for a registry.

Reset computational state of jobs.

showClusterStatus

Show information about available computational resources on cluster.

makeClusterFunctionsLSF

Create cluster functions for LSF systems.

Tests a job by running it with Rscript in a new process.

Loads result files for id vector.

makeClusterFunctions

Create a ClusterFuntions object.

Set and overwrite configuration settings

makeClusterFunctionsLocal

Create cluster functions for sequential execution on local host.

Sets the job function for already existing jobs.

ONLY FOR INTERNAL USAGE.

Wait for termination of jobs on the batch system.

Get job from registry by id.

makeClusterFunctionsInteractive

Create cluster functions for sequential execution in same session.

Grep log files for a pattern.

installPackagesOnSSHWorkers

Install packages on SSH workers.

removeRegistryPackages

Remove packages from registry.

makeClusterFunctionsMulticore

Use multiple cores on local Linux machine to spawn parallel jobs.

removeRegistrySourceDirs

Remove packages from registry.

makeClusterFunctionsOpenLava

Create cluster functions for OpenLava systems.

Create SSH worker for SSH cluster functions.

makeSubmitJobResult

Create a SubmitJobResult object.

Submit jobs or chunks of jobs to batch system via cluster function.

sourceRegistryFiles

Source registry files

batchMapResults

Maps a function over the results of a registry by using batchMap.

Export R object to be available on the slaves.

The BatchJobs package

Maps a function over lists or vectors, adding jobs to a registry.

Combination of makeRegistry, batchMap and submitJobs.

addRegistryPackages

Add packages to registry.

applyJobFunction

applyJobFunction ONLY FOR INTERNAL USAGE.

batchReduceResults

Reduces results via a binary function and adds jobs for this to a registry.